htslib

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tabix: how to retain header for arbitrary file types?

2

I'm creating tabix indexes for arbitrarily formatted GWAS summary stats. This works fine, but the header seems to be lost. If I pass `--skip-lines`, then when I query the header,...

carbocation

Random read error on google cloud.

4

I am using SeqLib to read in bam/cram files on a cloud instance. After compiling the library with gcloud support, most of the time reading in bam files works, however...

stefangroha

Proposal to add hts_log callback function and hts_log_set_logger()

2

A somewhat tidied-up version of @lczech's concrete proposal in #1397 for overriding the default printing of hts_log messages to stderr. Draft, as the new function (and associated typedef) would require...

jmarshall

hts_log_error() extension for better error reporting

5

Hi there! This is more of a general suggestion to improve error reporting, but I'll illustrate it with a concrete example. I have started using the sam/bam/cram functionality recently, and...

lczech

Iteration over SAM header lines and header expression filtering

2

A proposal to add API functions allowing user code to iterate over all header lines in order. Then with a way of referencing a particular generic header line established, we...

jmarshall

Obtain S3 credentials via IAM roles

23

In addition to the use case where a session token is provided as part of a Federated access model, probably the more common use case is for [using IAM roles...

jmarshall

Progress and Cancelation for Indexing

11

It would be really nice to be able to capture the progress of the indexing functions, especially for large files as this can take some time. Adding callbacks to the...

BickfordA

bcf_hdr_parse_line() and bcf_hrec_add_key() in vcf.c do not check for INFO and FORMAT keys matching VCF specifications

1

If I attempt to add a header string to a VCF header using `bcf_hdr_append()`, the string gets passed to the function `bcf_hdr_parse_line()` which parses the key and passes it to...

freeseek

[Documentation] Short examples?

1

Would it be possible to add a few fast-starter examples to htslib? Nothing too complicated, just perhaps 3-5 smallish example for people to quickly test htslib after they have compiled...

rubyFeedback

Confusing BCF error messages, and mixing warnings vs errors.

7

If I have a VCF file with a missing `##FORMAT` record, then a straight `bcftools view` issues a warning: ``` @ seq4-head2[tmp/vcf]; bcftools view passed_ploidy_001.vcf|wc [W::vcf_parse_format] FORMAT 'PL' at 1:61462...

jkbonfield